Locus 4236

Sequence ID 3R_DroMel_CAF1
Location 11,375,186 – 11,375,419
Length 233
Max. P 0.999129
window6866 window6867 window6868

overview

Window 6

Location 11,375,186 – 11,375,299
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.46
Mean single sequence MFE -41.88
Consensus MFE -38.16
Energy contribution -38.92
Covariance contribution 0.76
Combinations/Pair 1.27
Mean z-score -2.71
Structure conservation index 0.91
SVM decision value 3.39
SVM RNA-class probability 0.999129
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11375186 113 - 27905053
UCUACAUUGGGCAGUUUCCGGCAACGGUGACUAUUUACCAUGUAGAUGGCACUGUUGUGGUUACCCAUGGGGGCAUAGAAAUGGGUCAGGGUAAGUAAGGGAGCAGACUU-------UUA
.............((((((.(((((((((.((((((((...)))))))))))))))))(.((((((.....(((.((....)).))).)))))).)..))))))......-------... ( -38.30)
>DroSec_CAF1 122824 113 - 1
UCUACAUUGGGCAGUUUCCGGCAACAGUGACUAUUUACCAUGUCGAUGGCACUGUUGUGGUUACCCACGGGGGCAUAGAAAUGGGUCAGGGUGAGUAAGGGGACUGUCUU-------UCA
........(((((((..((.(((((((((.(((((.((...)).))))))))))))))(.((((((.....(((.((....)).))).)))))).)..))..))))))).-------... ( -43.50)
>DroSim_CAF1 113828 113 - 1
UCUACAUUGGGCAGUUUCCGGCAACGGUGACUAUUUACCAUGUGGAUGGCACUGUUGUGGUUACCCAUGGGGGCAUAGAAAUGGGUCAGGGUGAGUAAGGGAGCUGUCUU-------UCA
........(((((((((((.(((((((((.((((((((...)))))))))))))))))(.((((((.....(((.((....)).))).)))))).)..))))))))))).-------... ( -46.20)
>DroEre_CAF1 110382 112 - 1
UCUACAUCGGACAGUUUCCAGCAACGGUGACUAUUUACCAUGUGGAUGGCUCUGUUGUGGUUACUCAUGGGGGCAUUGAAAUGGGCCAGGGUGAGUAAG----CAGCUCUCCA----AUA
........(((.((((....(((((((.(.((((((((...))))))))).)))))))(.((((((((...(((..........)))...)))))))).----))))).))).----... ( -36.70)
>DroYak_CAF1 112916 120 - 1
UCUACAUAGGGCAGUUUCCGGCAACGGUGACUAUCUACCACGUGGAUGGCACUGUUGUGGUUACCCAUGGGGGCAUAGAAAUGGGUCAGGGUGAGUAAGGGAGCUACUUACCAUAGUAUA
..(((....(((.((((((.(((((((((.((((((((...))))))))))))))))).)...(((....)))....)))))..)))..((((((((.(....)))))))))...))).. ( -44.70)
>consensus
UCUACAUUGGGCAGUUUCCGGCAACGGUGACUAUUUACCAUGUGGAUGGCACUGUUGUGGUUACCCAUGGGGGCAUAGAAAUGGGUCAGGGUGAGUAAGGGAGCUGCCUU_______UUA
........(((((((((((.(((((((((.((((((((...)))))))))))))))))(.((((((.....(((.((....)).))).)))))).)..)))))))))))........... (-38.16 = -38.92 +   0.76)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,375,219 – 11,375,339
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.83
Mean single sequence MFE -41.30
Consensus MFE -38.72
Energy contribution -37.24
Covariance contribution -1.48
Combinations/Pair 1.31
Mean z-score -1.90
Structure conservation index 0.94
SVM decision value 2.95
SVM RNA-class probability 0.997880
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11375219 120 - 27905053
AAAAGAGGCUUGGGUCUCUCCUUGAUGAACUUCCCCAUUAUCUACAUUGGGCAGUUUCCGGCAACGGUGACUAUUUACCAUGUAGAUGGCACUGUUGUGGUUACCCAUGGGGGCAUAGAA
...((((((....))))))............((((((((((((((((.((..((((.(((....))).)))).....))))))))))).(((....))).......)))))))....... ( -40.60)
>DroSec_CAF1 122857 120 - 1
AAAAGAGGCUUGGGUCUCUCCUUGAUGAACUUCCCCGUCAUCUACAUUGGGCAGUUUCCGGCAACAGUGACUAUUUACCAUGUCGAUGGCACUGUUGUGGUUACCCACGGGGGCAUAGAA
...((((((....))))))(((.(((((.(......))))))......)))..((..((((((((((((.(((((.((...)).))))))))))))))((....)).)))..))...... ( -38.90)
>DroSim_CAF1 113861 120 - 1
AAAAGAGGUUUGGGUCUCUCUUUGAUGAACUUCCCCGUCAUCUACAUUGGGCAGUUUCCGGCAACGGUGACUAUUUACCAUGUGGAUGGCACUGUUGUGGUUACCCAUGGGGGCAUAGAA
.(((((((........)))))))........((((((((((((((((.((..((((.(((....))).)))).....)))))))))))))......((((....)))))))))....... ( -44.30)
>DroEre_CAF1 110414 120 - 1
AAAAGGGGCUUGGGCCUCUCCUUGAUGGACUUCCCCAUCAUCUACAUCGGACAGUUUCCAGCAACGGUGACUAUUUACCAUGUGGAUGGCUCUGUUGUGGUUACUCAUGGGGGCAUUGAA
...((((((....))))))..(..(((....(((((((..(((.....))).(((..(((.((((((.(.((((((((...))))))))).)))))))))..))).))))))))))..). ( -40.10)
>DroYak_CAF1 112956 120 - 1
AAAAGGGGCUUGGGUCUCUCCUUGAUGAACUUUCCCGUCAUCUACAUAGGGCAGUUUCCGGCAACGGUGACUAUCUACCACGUGGAUGGCACUGUUGUGGUUACCCAUGGGGGCAUAGAA
...((((((....))))))(((.(((((.(......)))))).....)))...((..((((((((((((.((((((((...)))))))))))))))))((....)).)))..))...... ( -42.60)
>consensus
AAAAGAGGCUUGGGUCUCUCCUUGAUGAACUUCCCCGUCAUCUACAUUGGGCAGUUUCCGGCAACGGUGACUAUUUACCAUGUGGAUGGCACUGUUGUGGUUACCCAUGGGGGCAUAGAA
...((((((....))))))...(((((........))))).............((..((((((((((((.((((((((...)))))))))))))))))((....)).)))..))...... (-38.72 = -37.24 +  -1.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,375,299 – 11,375,419
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.58
Mean single sequence MFE -37.87
Consensus MFE -32.81
Energy contribution -33.33
Covariance contribution 0.52
Combinations/Pair 1.13
Mean z-score -1.77
Structure conservation index 0.87
SVM decision value 1.66
SVM RNA-class probability 0.970671
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11375299 120 - 27905053
UUCCAGAGUUCCUCAAGACUAGGGAGUACUACUCCCGGAAGAAGGAGAUCGAGGCAUUCAAUGCCAACAAUCGAUGGAAAAAAAGAGGCUUGGGUCUCUCCUUGAUGAACUUCCCCAUUA
.....((((((.(((((....(((((.....))))).......(((((((.((((.(((....(((.(....).))).......))))))).))))))).))))).))))))........ ( -38.70)
>DroSec_CAF1 122937 120 - 1
UUCCAGAGUUCCUCAAGACUAGGGAGUACUACUCCCGGAAGAAGGAGAUCGAGAAAUUCAAUGCCAACAAUCGAUGGAAAAAAAGAGGCUUGGGUCUCUCCUUGAUGAACUUCCCCGUCA
.....(((...)))..(((..(((((.....)))))((..((((...((((((..........(((.(....).)))......((((((....)))))).))))))...)))).))))). ( -33.50)
>DroSim_CAF1 113941 120 - 1
UUCCAGAGUUCCUCAAGACUAGGGAGUACUACUCCCGGAAGAAGGAGAUCGAGGCAUUCAAUGCCAACAACCGAUGGAAAAAAAGAGGUUUGGGUCUCUCUUUGAUGAACUUCCCCGUCA
((((..((((......)))).(((((.....)))))))))((((((((((..(((((...)))))..(((((..(........)..)).))))))))).))))((((........)))). ( -36.70)
>DroEre_CAF1 110494 120 - 1
UUCCGGAGUUCCUCAAGACUAGGGAGUACUACUCCCGGAGGAAGGAGAUCGAGCAGUUCAAUGCCAACAACCGGUGGAAGAAAAGGGGCUUGGGCCUCUCCUUGAUGGACUUCCCCAUCA
..((((..((((((.......(((((.....))))).)))))).......(.(((......)))).....)))).(((((....(((((....)))))(((.....))))))))...... ( -41.90)
>DroYak_CAF1 113036 120 - 1
UUCCGGAGUUCCUCAAGACUAGGGAGUACUACUCCCGGCGGAAGGAGAUCGAGGUAUUCAACGCCAACAACCGAUGGAAAAAAAGGGGCUUGGGUCUCUCCUUGAUGAACUUUCCCGUCA
...((((((((.(((((....(((((.....))))).......(((((((.((((........(((.(....).)))..........)))).))))))).))))).)))))...)))... ( -38.57)
>consensus
UUCCAGAGUUCCUCAAGACUAGGGAGUACUACUCCCGGAAGAAGGAGAUCGAGGAAUUCAAUGCCAACAACCGAUGGAAAAAAAGAGGCUUGGGUCUCUCCUUGAUGAACUUCCCCGUCA
.....((((((.(((((....(((((.....))))).......(((((((.((((........(((.(....).)))..........)))).))))))).))))).))))))........ (-32.81 = -33.33 +   0.52)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:01 2006